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Because there is no moon
This has been discussed before, and it's really very strange but if you pay attention you'll notice that in spite of the many shots of the starry sky that we got never once you can see the moon in them.

It could be just a coincidence or just an error, but it is very suspicious.

I sure hope the lack of a moon is a coincidence or an error because the scientific implications of Earth actually losing its moon goes well beyond anything the series has demonstrated at this point. No more moon = calamity on a huge scale.

Because there is no moon
This has been discussed before, and it's really very strange but if you pay attention you'll notice that in spite of the many shots of the starry sky that we got never once you can see the moon in them.

It could be just a coincidence or just an error, but it is very suspicious.

I didn't notice that. Wow, if there's no moon, then just what happened in the past X years? That probably leaves plenty of room to explain the condition of the planet?

Lack of a moon would make the planet more susceptible to foreign projectiles. Maybe all their satellites were destroyed by another species or random space objects, and then the planet was bombarded with comets that melted to form the ocean planet.

The lack of moon also reduces the tidal forces and make earth's tilt more sensitive to other masses like Jupiter. Maybe the earth isn't on a tilt any more and season-less.

If the Earth never had a moon or had only small moons like Phobos & Deimos, then that would be one thing. Presumably Earth's environment and geology would still have stabilized albeit into a very different world than our current one. However, I believe that to tear the current moon away from the Earth now would cause severe changes Earth's stability and that life on Earth would suffer severe trials in the process. I don't argue that the Earth could eventually find a stable situation without the moon. I argue that the transition to that new stable situation would be bad for life as we know it and as Gargantia depicts it. Very, very bad.

Well but the Earth of this anime did suffer severe calamities. A total glaciation and the transformation into a water planet have probably been even more catastrophic events than anything that the sudden removal of the moon would cause.

Of course I have no doubts that the transition from no moon would be catastrophic, but we're dealing with an even worse scenario here.
This Earth already recovered from something worse than that. I don't expect all this to have happened in less than at least several centuries.

Okay, I don't think cloning is involved after watching episode 9: I think the eugenics approach of the GA was created to both combat the idea of genetic manipulation ala the Evolvers and to combat humans adapting to space.

It's been proven that space travel, especially long periods of it can have detrimental effects on humans. The Evolvers relied on genetic manipulation, becoming something beyond human. The rest of humanity, disgusted by what their fellow man had become, decided on eugenics. The war with the Hideauze/Evolvers serves two purposes: a way of annihilation against those who gave up their humanity and a way to sift the wheat. The weak die in battle and those who survive their 16th birthday are deemed the strong and allowed to procreate and create a stronger generation. Those born weak are disposed of and the cycle continues. Scary stuff

I'm just interested in whale-squid.... are they actually ever exist as animal before?

from what I've understood, there's actually a kind of squid (symbiont or whatever), then they're engineered by mixing them with humans

To sum it up:

The scientists of the Evolver faction created an artificial life form: the Symbiot.

The Symbiot:
-kinda resembles a squid, though amusingly a starfish as well (the way they sucked on the walls of their tank).
-appears to be an autotrophic life form (like plants, and corals to some extent), meaning they don't need to feed on organic matter: light and inorganic nutriments are enough.
-it relies on symbiotic nanomachines which excell at converting sunlight into electricity (unclear on how this relation feed them)
-instead of an unnecessary gastrointestinal tract, it has a cavity designed to envelop, support and provide control to a Homo Sapiens

These symbiots were worn by Humans of the Evolver faction to become the 1st generation of Whalesquid/Hideauze. From how they and later individuales are depicted:
-they can produce electricity with their nanomachines
-they can electrolyse water into hydrogen and oxygen
-reproduction is done by what appear to be "Queens": the female "human" core likely produces fertilized eggs, which are processed by the Symbiot into combined "eggs".
-an egg's maturation, more or less equivalent to a pregnancy (probably covering infancy as well), resembles the hydrozoan's polyp life stage.
-"human" cores appear more and more fused with the symbiot as they mature ("face" and fangs).
-unclear if the human core continues to grows, if there's an atrophy of core limbs and/or a suppression/mitigation of bone calcification.

On space Hideauze, we know that:
-they have multiple forms, including large planetoid sized colonies (those probably develop by gathering water in order to provide a breeding ground for the colony)
-they develop a massive shell of nanomachines
-they can produce beams